Reaction coordinate

A reaction coordinate is a chemical abstract dimensional coordinate representing the progress along the reaction path. It is usually a geometrical parameter which changes during the conversion of one or more molecular entities ( substances).

In molecular dynamics simulations reaction coordinates that describe the folding state of a protein are referred to as Collective Variables.

These coordinates can sometimes be easily displayed in the spatial domain ( bond length, bond angles, ... ). However, this is more complex for the reaction coordinate difficult, especially when non- geometric parameters are used, for example, the bond order.

Reaction coordinates are often plotted against the free energy, the energy profiles that pass through during the reaction by an energy diagram to demonstrate.